TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms

  • EMBO J. 2015 Jul 2;34(13):1801-15. doi: 10.15252/embj.201590931.
Boseon Kim  1 ,  Minju Ha  1 ,  Luuk Loeff  2 ,  Hyeshik Chang  1 ,  Dhirendra K Simanshu  3 ,  Sisi Li  3 ,  Mohamed Fareh  2 ,  Dinshaw J Patel  3 ,  Chirlmin Joo  4 ,  V Narry Kim  5
Affiliations
  • 1. Center for RNA Research, Institute for Basic Science, Seoul, Korea School of Biological Sciences, Seoul National University, Seoul, Korea.
  • 2. Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands.
  • 3. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
  • 4. Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands [email protected] [email protected].
  • 5. Center for RNA Research, Institute for Basic Science, Seoul, Korea School of Biological Sciences, Seoul National University, Seoul, Korea [email protected] [email protected].
PMID: 25979828 DOI: 10.15252/embj.201590931
Abstract

Terminal uridylyl transferases (TUTs) function as integral regulators of MicroRNA (miRNA) biogenesis. Using biochemistry, single-molecule, and deep Sequencing techniques, we here investigate the mechanism by which human TUT7 (also known as ZCCHC6) recognizes and uridylates precursor miRNAs (pre-miRNAs) in the absence of Lin28. We find that the overhang of a pre-miRNA is the key structural element that is recognized by TUT7 and its paralogues, TUT4 (ZCCHC11) and TUT2 (GLD2/PAPD4). For group II pre-miRNAs, which have a 1-nt 3' overhang, TUT7 restores the canonical end structure (2-nt 3' overhang) through mono-uridylation, thereby promoting miRNA biogenesis. For pre-miRNAs where the 3' end is further recessed into the stem (as in 3' trimmed pre-miRNAs), TUT7 generates an oligo-U tail that leads to degradation. In contrast to Lin28-stimulated oligo-uridylation, which is processive, a distributive mode is employed by TUT7 for both mono- and oligo-uridylation in the absence of Lin28. The overhang length dictates the frequency (but not duration) of the TUT7-RNA interaction, thus explaining how TUT7 differentiates pre-miRNA species with different overhangs. Our study reveals dual roles and mechanisms of uridylation in repair and removal of defective pre-miRNAs.

Keywords
TUT4 (ZCCHC11); TUT7 (ZCCHC6); precursor microRNA; single‐molecule fluorescence; uridylation.